First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus

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dc.authorid0000-0001-9797-7536en_US
dc.authorid0000-0002-5836-8030en_US
dc.contributor.authorAkbaş, Birol
dc.contributor.authorMorca, Ali Ferhan
dc.contributor.authorÇoşkan, Sevgi
dc.contributor.authorSantosa, Adyatma Irawan
dc.contributor.authorKılıç, Handan Çulal
dc.contributor.authorÇelik, Ali
dc.date.accessioned2024-07-09T08:30:05Z
dc.date.available2024-07-09T08:30:05Z
dc.date.issued2023en_US
dc.departmentBAİBÜ, Ziraat Fakültesi, Bitki Koruma Bölümüen_US
dc.descriptionThis study was funded by the General Directorate of Agricultural Research and Policies, Directorate of Central Plant Protection Research Institute, and the Head of Rural Service Department, Ankara Metropolitan Municipality. The authors also would like to thank the Ankara Directorate of Provincial Agriculture and Forestry and the Republic of Turkey Ministry of Agriculture and Forestry for their assistance during field surveys.en_US
dc.description.abstractThe complete genome of plum pox virus strain T isolates from five different Prunus spp., including almond (P. dulcis) and sour cherry (P. ceracus) isolates, was fully sequenced using the primer pairs designed in this study. The five isolates were aligned with other 50 PPV-T isolates whose complete genome sequences were available in GenBank and then subjected to phylogenetic and diversity analyses. Recombination analysis showed no significant signal detected in the five newly sequenced isolates while confirming four recombinant isolates reported in a previous study. Nucleotide and amino acid phylogenetic trees clustered the tested isolates into three major groups: Balkan 1, 2, and 3. Strain T isolates shared high nucleotide and amino acid identities among them. Diversity analysis applied different parameters to found that the sequences of P3 and 6K1 genes were more conserved over other genes. In accordance, the highly variable P1 and CP genes were found to experience weaker purifying pressures, ? = 0.127 and 0.219, respectively, than other genes. The three neutrality tests gave negative values to all genes, suggesting that strain T populations have expanding or bottleneck selections. Genetic make-up of the only known sour cherry isolate is highly identical to isolates from other Prunus spp. Therefore, this study has updated our knowledge of T strain diversity in new hosts and provided a clear picture of genetic variation and host relationships.en_US
dc.description.sponsorshipThis study was funded by the General Directorate of Agricultural Research and Policies, Directorate of Central Plant Protection Research Institute, and the Head of Rural Service Department, Ankara Metropolitan Municipality. The authors also would like to t; General Directorate of Agricultural Research and Policies, Directorate of Central Plant Protection Research Instituteen_US
dc.identifier.citationAkbaş, B., Morca, A. F., Coşkan, S., Santosa, A. I., Çulal-Kılıç, H., & Çelik, A. (2023). First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus. 3 Biotech, 13(10), 332.en_US
dc.identifier.doi10.1007/s13205-023-03746-1
dc.identifier.endpage8en_US
dc.identifier.issn2190-572X
dc.identifier.issn2190-5738
dc.identifier.issue10en_US
dc.identifier.pmid37681114en_US
dc.identifier.scopus2-s2.0-85169691949en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage1en_US
dc.identifier.urihttp://dx.doi.org/10.1007/s13205-023-03746-1
dc.identifier.urihttps://hdl.handle.net/20.500.12491/12245
dc.identifier.volume13en_US
dc.identifier.wosWOS:001062171300003en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorÇelik, Ali
dc.language.isoenen_US
dc.publisherSpringer Heidelbergen_US
dc.relation.ispartof3 Biotechen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectDiversity and Polymorphism Analysesen_US
dc.subjectNeutrality Testsen_US
dc.subjectPhylogenetic Analysisen_US
dc.subjectRecombination Analysisen_US
dc.subjectRT-PCRen_US
dc.titleFirst complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasusen_US
dc.typeArticleen_US

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